Hi Omer,
You use a dielectric constant is 80, which means that the electrostatic
interactions are screened. Perhaps that's why your density is low.
Ran.
Omer Markovitch wrote:
> Dear All,
> I have simulated a protein inside a box with water and ions. I began
> by minimizing my system (which has a total charge of zero), until the
> maximum gradient was small enough and the potential energy become
> negative.
> Then I heated it, slowly, to 300K at constant volume (using berendsen
> thermostat and tcoupl = 1 ps).
> Then I performed 500 ps NVT simulation to equilibrate the temperature,
> at 300K.
> Then, I tried to equilibrate the pressure and run NPT simulation,
> using Berendsen barostat (p=1, pcoupl=10) and Berendsen thermostat
> (T=300K, tcoupl = 0.1).
>
> My problem is, that with the barostat & thermostat both active in the
> same MD run, my density drops to a very low value (at the first MD
> steps, the density is 1000, dropping later to 100 kg/m^3). That is- my
> box dimensions increase significantly (from around 6x6x6 to 12x12x12
> nm^3. If I change the pressure coupling constant, the speed of the
> expansion changes but all simulation converged to a small density
> between 50-100 kg/m3.
>
> Your help is appreciated; Probably, I am not controlling the
> simulation like I should. I will appreciate any advice.
> Thank you, Omer Markovitch.
>
> I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run:
>
> integrator = md
> dt = 0.001
> nsteps = 50
> comm_grps= system
> nstxout = 500
> nstvout = 500
> nstcheckpoint= 1000
> nstlog = 500
> nstenergy= 500
> nstlist = 10
> ns_type = simple
> pbc = xyz
> rlist= 1.0
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 1.0
> epsilon_r= 80
> epsilon_rf = 80
> vdw-type = Cut-off
> rvdw-switch = 0
> rvdw = 1.0
> table-extension = 1
> fourierspacing = 0.12
> pme_order= 4
> ewald_rtol = 1e-05
> ewald_geometry = 3d
> optimize_fft = yes
> tcoupl = berendsen
> tc-grps = system
> tau_t= 0.1
> ref_t= 300
> Pcoupl = berendsen
> Pcoupltype = Isotropic
> tau-p= 10
> compressibility = 4.5E-5
> ref-p= 1
> andersen_seed= 815131
> constraints = none
>
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
